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PubMed2002

Discovery and phylogenetic analysis of a riverine species flock of African electric fishes (Mormyridae: Teleostei).

The evolution of species-specific mate recognition signals is of particular interest within speciose monophyletic groups with restricted distributions (known as "species flocks"). However, the explosive nature of speciation in these clades makes difficult the reconstruction of their phylogenetic history. Here we describe a species flock of riverine mormyrid fishes from west-central Africa in which electric signals may play a role in the reproductive isolation of sympatric species. In our recent field collections, totaling more than 1400 specimens from many localities, we recognize 38 forms that are distinct in their morphologies and electric organ discharge (EOD) characteristics. Of these 38, only four clearly correspond to described species. Here we treat these forms as operational taxonomic units (OTUs) in a phylogenetic analysis of cytochrome b sequence data from a sample of 86 specimens. We examined support in the molecular data for the monophyly of these 38 OTUs considered together, the monophyly of each phenotypically delimited OTU considered individually, and for relationships among OTUs congruent with those inferred from the distribution of morphological and EOD character states. Trees obtained by both maximum-parsimony and maximum-likelihood analyses, rooted with sequence data from outgroup taxa, provide evidence for the monophyly of these 38 OTUs with respect to other mormyrid fishes. The small genetic distances between many distinct forms suggest their recent divergence. However, in many instances the cytochrome b tree topology fails to support the monophyly of individual OTUs and close relationships between OTUs that are similar in morphology and EOD characteristics. In other cases, individuals from distinct OTUs share identical or nearly identical haplotypes. Close examination of these cases suggests that unnatural OTU definition is not the sole cause of this pattern, and we infer an incongruence between the mitochondrial gene tree and the organismal phylogeny caused by incomplete mitochondrial lineage sorting and/ or introgression across forms. The apparently rapid diversification in this clade of riverine electric fishes and the problems associated with recovering a meaningful species-level phylogeny from mitochondrial data parallel findings in other species flocks. Selection on EOD waveforms as mate recognition signals may be involved in the radiation of these fishes. This is the first description of a freshwater fish species flock from a riverine, as opposed to a lacustrine, environment.

Animals↗

PubMed1998

Phylogenetic utility of the external transcribed spacer (ETS) of 18S-26S rDNA: congruence of ETS and ITS trees of Calycadenia (Compositae).

The 3' region of the external transcribed spacer (ETS) of 18S-26S nuclear ribosomal DNA was sequenced in 19 representatives of Calycadenia/Osmadenia and two outgroup species (Compositae) to assess its utility for phylogeny reconstruction compared to rDNA internal transcribed spacer (ITS) data. Universal primers based on plant, fungal, and animal sequences were designed to amplify the intergenic spacer (IGS) and an angiosperm primer was constructed to sequence the 3' end of the ETS in members of tribe Heliantheae. Based on these sequences, an internal ETS primer useful across Heliantheae sensu lato was designed to amplify and sequence directly the 3' ETS region in the study taxa, which were the subjects of an earlier phylogenetic investigation based on ITS sequences. Size variation in the amplified ETS region varied across taxa of Heliantheae sensu lato from approximately 350 to 700 bp, in part attributable to an approximately 200-bp tandem duplication in a common ancestor of Calycadenia/Osmadenia. Phylogenetic analysis of the 200-bp subrepeats and examination of apomorphic changes in the duplicated region demonstrate that the subrepeats in Calycadenia/Osmadenia have evolved divergently. Phylogenetic analyses of the entire amplified ETS region yielded a highly resolved strict consensus tree that is nearly identical in topology to the ITS tree, with strong bootstrap and decay support on most branches. Parsimony analyses of combined ETS and ITS data yielded a strict consensus tree that is better resolved and generally better supported than trees based on either data set analyzed separately. We calculated an approximately 1.3- to 2.4-fold higher rate of sequence evolution by nucleotide substitution in the ETS region studied than in ITS-1 + ITS-2. A similar disparity in the proportion of variable (1.3 ETS:1 ITS) and potentially informative (1.5 ETS:1 ITS) sites was observed for the ingroup. Levels of homoplasy are similar in the ETS and ITS data. We conclude that the ETS holds great promise for augmenting ITS data for phylogenetic studies of young lineages.

Base Sequence↗

PubMed2003

Systematics of the lizard family pygopodidae with implications for the diversification of Australian temperate biotas.

We conducted a phylogenetic study of pygopodid lizards, a group of 38 species endemic to Australia and New Guinea, with two major goals: to reconstruct a taxonomically complete and robustly supported phylogeny for the group and to use this information to gain insights into the tempo, mode, and timing of the pygopodid radiation. Phylogenetic analyses of mitochondrial DNA (mtDNA), nuclear DNA (nDNA), and previously published morphological data using parsimony, maximum likelihood, and Bayesian methods on the independent and combined three data sets yielded trees with similar and largely stable ingroup topologies. However, relationships among the six most inclusive and unambiguously supported clades (Aprasia, Delma, Lialis, Ophidiocephalus, Pletholax, and Pygopus) varied depending on data set analyzed. We used parametric bootstrapping to help us understand which of the three-branch schemes linking these six taxa was most plausible given our data. We conclude based on our results that the arrangement ((((Delma, Lialis)Pygopus)Pletholax)(Aprasia, Ophidiocephalus)) represents the best hypothesis of intergeneric relationships. A second major problem to arise in our study concerned the inability of our two outgroup taxa (Diplodactylus) to root trees properly; three different rooting locations were suggested depending upon analysis. This long-branch attraction problem was so severe that the outgroup branch also interfered with estimation of ingroup relationships. We therefore used the molecular clock method to root the pygopodid tree. Results of two independent molecular clock analyses (mtDNA and nDNA) converged upon the same root location (branch leading to Delma). We are confident that we have found the correct root because the possibility of our clock estimates agreeing by chance alone is remote given that there are 65 possible root locations (branches) on the pygopodid tree (approximately 1 in 65 odds). Our analysis also indicated that Delma fraseri is not monophyletic, a result supported by a parametric bootstrapping test. We elevated the Western Australian race, Delma f. petersoni, to species status (i.e., Delma petersoni) because hybridization and incomplete lineage sorting could be ruled out as potential causes of this paraphyletic gene tree and because D. grayii is broadly sympatric with its sister species D. fraseri. Climate changes over the past 23 million years, which transformed Australia from a wet, green continent to one that is largely dry and brown, have been suspected as playing a major role in the diversification of Australia's temperate biotas. Our phylogenetic analyses of pygopodid speciation and biogeography revealed four important findings consistent with this climate change diversification model: (1) our fossil-calibrated phylogeny shows that although some extant pygopodid lineages predate the onset of aridification, 28 of 33 pygopodid species included in our study seem to have originated in the last 23 million years; (2) relative cladogenesis tests suggest that several major clades underwent higher than expected rates of speciation; (3) our findings support earlier studies showing that speciation of mesic-adapted biotas in the southeastern and southwestern corners of Australia largely occurred within each of these regions between 12 and 23 million years ago as opposed to repeated dispersal between these regions; and (4) we have identified for the first time the existence of several pairs of sympatric sister species of lizards living in arid and semiarid ecosystems. These sympatric sister species seem to be younger than allopatric or parapatric sister-species pairs, which is not consistent with previous beliefs.

Animals↗

PubMed2006

Co-cladogenesis spanning three phyla: leafhoppers (Insecta: Hemiptera: Cicadellidae) and their dual bacterial symbionts.

Endosymbioses are a major form of biological complexity affecting the ecological and evolutionary diversification of many eukaryotic groups. These associations are exemplified by nutritional symbioses of insects for which phylogenetic studies have demonstrated numerous cases of long-term codiversification between a bacterial and a host lineage. Some insects, including most leafhoppers (Insecta: Hemiptera: Cicadellidae), have more than one bacterial symbiont within specialized host cells, raising questions regarding the patterns of codiversification of these multiple partners and the evolutionary persistence of complex symbiotic systems. Previous studies reported the presence of two dominant symbiont types in a member of the leafhopper subfamily Cicadellinae (sharpshooters). In this study, 16S rRNA sequences were obtained and used to examine the occurrence and evolutionary relationships of the two dominant symbiont types across 29 leafhopper species. Candidatus Sulcia muelleri (Bacteroidetes) was detected in all leafhopper species examined, a finding that is consistent with a previous report of its ancient association with the Auchenorrhyncha (a grouping that includes leafhoppers, treehoppers, cicadas, planthoppers, and spittlebugs). Baumannia cicadellinicola (Proteobacteria), previously known from only five sharpshooter species, was found only in the sharpshooter tribes Cicadellini and Proconiini, as well as in the subfamily Phereurhininae. Mitochondrial and nuclear gene sequences were obtained and used to reconstruct host phylogenies. Analyses of host and symbiont data sets support a congruent evolutionary history between sharpshooters, Sulcia and Baumannia and thus provide the first strong evidence for long-term co-inheritance of multiple symbionts during the diversification of a eukaryotic host. Sulcia shows a fivefold lower rate of 16S rDNA sequence divergence than does Baumannia for the same host pairs. The term 'coprimary' symbiont is proposed for such cases.

Animals↗

PubMed2004

The genus Spiroplasma and its non-helical descendants: phylogenetic classification, correlation with phenotype and roots of the Mycoplasma mycoides clade.

The genus Spiroplasma (helical mollicutes: Bacteria: Firmicutes: Mollicutes: Entomoplasmatales: Spiroplasmataceae) is associated primarily with insects. The Mycoplasma mycoides cluster (sensu Weisburg et al. 1989 and Johansson and Pettersson 2002) is a group of mollicutes that includes the type species - Mycoplasma mycoides - of Mycoplasmatales, Mycoplasmataceae and Mycoplasma. This cluster, associated solely with ruminants, contains five other species and subspecies. Earlier phylogenetic reconstructions based on partial 16S rDNA sequences and a limited sample of Spiroplasma and Mycoplasma sequences suggested that the genus Mycoplasma was polyphyletic, as the M. mycoides cluster and the grouping that consisted of the hominis and pneumoniae groups of Mycoplasma species were widely separated phylogenetically and the M. mycoides cluster was allied with Spiroplasma. It is shown here that the M. mycoides cluster arose from Spiroplasma through an intermediate group of non-helical spiroplasmal descendants - the Entomoplasmataceae. As this conclusion has profound implications in the taxonomy of Mollicutes, a detailed phylogenetic study of Spiroplasma and its non-helical descendants was undertaken. These analyses, done with maximum-parsimony, provide cladistic status; a new nomenclature is introduced here, based on 'bottom-up' rather than 'top-down' clade classification. The order Entomoplasmatales consists of four major clades: (i) the Mycoides-Entomoplasmataceae clade, which contains M. mycoides and its allies and Entomoplasma and Mesoplasma species and is a sister lineage to (ii) the Apis clade of Spiroplasma. Spiroplasma and the Entomoplasmataceae are paraphyletic, but this status does not diminish their phylogenetic usefulness. Five species that were previously unclassified phylogenetically are basal to the Apis clade sensu strictu and to the Mycoides clade. One of these species, Spiroplasma sp. TIUS-1, has very poor helicity and a very small genome (840 kbp); this putative species can be envisioned as a 'missing link' in the evolution of the Mycoides-Entomoplasmataceae clade. The other two Spiroplasma clades are: (iii) the Citri-Chrysopicola-Mirum clade (serogroups I, II, V and VIII) and (iv) the ixodetis clade (serogroup VI). As Mesoplasma lactucae represents a basal divergence within the Mycoides-Entomoplasmataceae clade, and as Entomoplasma freundtii is basal to the Mycoides clade, M. mycoides and its allies must have arisen from an ancestor in the Entomoplasmataceae. The paraphyletic grouping that consists of the Hominis and Pneumoniae groups (sensu Johansson & Pettersson 2002) of Mycoplasma species contains the ancestral roots of Ureaplasma spp. and haemoplasmas. This clade is a sister lineage to the Entomoplasmatales clade. Serological classifications of spiroplasma are very highly supported by the trees presented. Genome size and G+C content of micro-organismal DNA were moderately conserved, but there have been frequent and polyphyletically distributed genome reductions. Sterol requirements were polyphyletic, as was the ability to grow in the presence of polyoxyethylene sorbitan-supplemented, but not serum-supplemented, media. As this character is not phylogenetically distributed, Mesoplasma and Entomoplasma should be combined into a single genus. The phylogenetic trees presented here confirm previous reports of polyphyly of the genus Mycoplasma. As both clades of Mycoplasma contain several species of great practical importance, a change of the genus name for species in either clade would have immense practical implications. In addition, a change of the genus name for M. mycoides would have to be approved by the Judicial Commission. For these reasons, the Linnaean and phylogenetic classifications of Mycoplasma must for now be discrepant.

Base Composition↗